Contacts of the strand formed by residues 226 - 231 (chain A) in PDB entry 4RG1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 2.9 42.2 + - - -
151A CYS* 4.1 11.9 - - - +
152A PRO* 3.7 24.6 - - - +
155A LEU* 4.5 5.6 - - + +
159A PHE* 3.6 30.6 - - + -
179A HIS* 3.9 1.8 - - - -
191A GLU* 2.8 36.5 + - - +
192A GLY 3.3 11.7 - - - +
224A GLY 3.7 1.8 + - - -
225A LEU* 1.3 75.0 - - - +
227A VAL* 1.3 66.2 + - - +
402A 15P 3.8 25.8 + - - -
403A 15P 4.0 4.5 - - - -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ARG 4.0 0.2 - - - +
191A GLU* 3.5 8.3 - - - +
192A GLY 2.8 36.3 + - - +
194A VAL* 4.4 14.6 - - + -
207A VAL* 3.9 23.6 - - + -
221A LEU* 3.9 26.2 - - + -
225A LEU* 4.4 6.3 - - + +
226A ARG* 1.3 81.0 - - - +
228A THR* 1.3 61.0 + - - +
229A VAL* 3.9 10.5 - - + -
246A VAL* 4.1 20.6 - - + -
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Residues in contact with THR 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PHE* 4.4 7.2 - - + -
190A ARG 3.8 2.7 - - - +
191A GLU* 2.6 25.4 + - - +
227A VAL* 1.3 73.1 - - - +
229A VAL* 1.3 63.2 + - - +
246A VAL* 3.4 6.6 - - - +
247A VAL* 3.0 51.1 + - + +
249A SER* 3.3 26.0 - - - -
252A PRO* 4.0 18.2 - - + -
260A TRP* 3.6 15.9 + - + +
403A 15P 4.5 0.2 - - - -
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PHE* 3.2 8.1 - - - +
190A ARG 2.8 39.8 + - - +
207A VAL* 4.3 4.9 - - + -
209A CYS* 3.8 22.4 - - - -
215A VAL* 3.9 25.1 - - + -
217A ILE* 4.4 5.4 - - + -
227A VAL* 3.9 21.1 - - + +
228A THR* 1.3 78.8 - - - +
230A ARG* 1.3 66.7 + - - +
231A LEU* 3.8 8.1 + - + +
244A GLY* 4.0 1.8 - - - -
245A LYS 3.5 20.6 - - - +
246A VAL* 4.5 8.7 - - + -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLU* 2.9 42.6 + - + +
189A PHE* 3.9 20.4 - - + -
228A THR 4.2 0.6 + - - -
229A VAL* 1.3 71.4 - - - +
231A LEU* 1.3 78.3 + - - +
232A ASN* 4.4 4.6 + - - +
233A GLN* 4.9 11.5 - - - +
244A GLY* 3.2 0.9 - - - -
245A LYS* 2.8 38.5 + - + +
247A VAL* 3.9 21.1 - - + +
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A SER 4.1 11.4 - - - +
188A GLU* 3.1 22.6 + - - +
190A ARG* 4.1 30.3 - - + +
209A CYS* 5.7 0.2 - - - -
211A MET* 4.1 18.4 - - + -
215A VAL* 4.0 31.9 - - + -
229A VAL* 3.9 15.3 - - + +
230A ARG* 1.3 89.0 + - - +
232A ASN* 1.3 68.4 + - - +
233A GLN* 3.6 1.7 + - - -
235A GLN* 4.5 3.1 - - - +
242A TYR* 4.4 6.3 - - + -
243A HIS 3.9 13.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il